Water in protein hydration and ligand recognition

M Maurer, C Oostenbrink - Journal of Molecular Recognition, 2019 - Wiley Online Library
This review describes selected basics of water in biomolecular recognition. We focus on a
qualitative understanding of the most important physical aspects, how these change in …

Water molecules at protein–drug interfaces: computational prediction and analysis methods

ML Samways, RD Taylor, HEB Macdonald… - Chemical Society …, 2021 - pubs.rsc.org
The fundamental importance of water molecules at drug–protein interfaces is now widely
recognised and a significant feature in structure-based drug design. Experimental methods …

Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines

Q Meng, C Ramírez-Palacios, N Capra… - ACS …, 2021 - ACS Publications
ω-Transaminases (ω-TA) are attractive biocatalysts for the production of chiral amines from
prochiral ketones via asymmetric synthesis. However, the substrate scope of ω-TAs is …

[HTML][HTML] The role of water in ligand binding

BZ Zsidó, C Hetényi - Current Opinion in Structural Biology, 2021 - Elsevier
Exploration of the complex modulatory role of water in ligand–target binding is a current
challenge of drug design. This review reports on recent advances of prediction of water …

The advances and limitations of the determination and applications of water structure in molecular engineering

BZ Zsidó, B Bayarsaikhan, R Börzsei, V Szél… - International Journal of …, 2023 - mdpi.com
Water is a key actor of various processes of nature and, therefore, molecular engineering
has to take the structural and energetic consequences of hydration into account. While the …

Heterogeneous and allosteric role of surface hydration for protein–ligand binding

J Shi, JH Cho, W Hwang - Journal of Chemical Theory and …, 2023 - ACS Publications
Atomistic-level understanding of surface hydration mediating protein–protein interactions
and ligand binding has been a challenge due to the dynamic nature of water molecules near …

Assessing the predictive power of relative binding free energy calculations for test cases involving displacement of binding site water molecules

J Wahl, M Smiesko - Journal of chemical information and …, 2019 - ACS Publications
Improved sampling methodologies, more accurate force fields, and access to longer
simulation time scales have led to an increased application of Relative Binding Free Energy …

Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics

W Chen, H He, J Wang, J Wang… - Physical Chemistry …, 2023 - pubs.rsc.org
Developing a ligand with high affinity for a specific protein target is essential for drug design,
and water molecules are well known to play a key role in protein–drug recognition …

Protein–ligand complex solvation thermodynamics: Development, parameterization, and testing of GIST-based solvent functionals

T Hüfner-Wulsdorf, G Klebe - Journal of Chemical Information …, 2020 - ACS Publications
In drug design, the importance of molecular solvation and desolvation is increasingly
appreciated and water molecules are recognized as active contributors to protein–ligand …

Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study

S Reyaz, A Tasneem, GP Rai, HR Bairagya - Journal of Molecular Graphics …, 2021 - Elsevier
The main protease (Mpro) is the key enzyme of nCOVID-19 and plays a decisive role that
makes it an attractive drug target. Multiple analysis of crystal structures reveals the presence …